7-5308283-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001080495.3(TNRC18):​c.8730C>T​(p.Asp2910Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 1,611,854 control chromosomes in the GnomAD database, including 22,717 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 1641 hom., cov: 33)
Exomes 𝑓: 0.17 ( 21076 hom. )

Consequence

TNRC18
NM_001080495.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.44
Variant links:
Genes affected
TNRC18 (HGNC:11962): (trinucleotide repeat containing 18) Predicted to enable chromatin binding activity. Located in cytosol; mitochondrion; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
Variant 7-5308283-G-A is Benign according to our data. Variant chr7-5308283-G-A is described in ClinVar as [Benign]. Clinvar id is 1250212.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.44 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TNRC18NM_001080495.3 linkc.8730C>T p.Asp2910Asp synonymous_variant Exon 30 of 30 ENST00000430969.6 NP_001073964.2 O15417-1A3KMH2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TNRC18ENST00000430969.6 linkc.8730C>T p.Asp2910Asp synonymous_variant Exon 30 of 30 5 NM_001080495.3 ENSP00000395538.1 O15417-1
TNRC18ENST00000399537.8 linkc.8730C>T p.Asp2910Asp synonymous_variant Exon 30 of 30 5 ENSP00000382452.4 H9KVB4

Frequencies

GnomAD3 genomes
AF:
0.137
AC:
20858
AN:
152114
Hom.:
1641
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0659
Gnomad AMI
AF:
0.0482
Gnomad AMR
AF:
0.170
Gnomad ASJ
AF:
0.145
Gnomad EAS
AF:
0.104
Gnomad SAS
AF:
0.0930
Gnomad FIN
AF:
0.207
Gnomad MID
AF:
0.133
Gnomad NFE
AF:
0.169
Gnomad OTH
AF:
0.134
GnomAD3 exomes
AF:
0.149
AC:
36288
AN:
244034
Hom.:
2928
AF XY:
0.148
AC XY:
19694
AN XY:
132694
show subpopulations
Gnomad AFR exome
AF:
0.0596
Gnomad AMR exome
AF:
0.163
Gnomad ASJ exome
AF:
0.134
Gnomad EAS exome
AF:
0.0943
Gnomad SAS exome
AF:
0.0921
Gnomad FIN exome
AF:
0.205
Gnomad NFE exome
AF:
0.171
Gnomad OTH exome
AF:
0.141
GnomAD4 exome
AF:
0.166
AC:
242268
AN:
1459622
Hom.:
21076
Cov.:
35
AF XY:
0.164
AC XY:
118844
AN XY:
725928
show subpopulations
Gnomad4 AFR exome
AF:
0.0581
Gnomad4 AMR exome
AF:
0.166
Gnomad4 ASJ exome
AF:
0.142
Gnomad4 EAS exome
AF:
0.102
Gnomad4 SAS exome
AF:
0.0946
Gnomad4 FIN exome
AF:
0.199
Gnomad4 NFE exome
AF:
0.177
Gnomad4 OTH exome
AF:
0.157
GnomAD4 genome
AF:
0.137
AC:
20853
AN:
152232
Hom.:
1641
Cov.:
33
AF XY:
0.139
AC XY:
10349
AN XY:
74418
show subpopulations
Gnomad4 AFR
AF:
0.0658
Gnomad4 AMR
AF:
0.170
Gnomad4 ASJ
AF:
0.145
Gnomad4 EAS
AF:
0.105
Gnomad4 SAS
AF:
0.0935
Gnomad4 FIN
AF:
0.207
Gnomad4 NFE
AF:
0.169
Gnomad4 OTH
AF:
0.133
Alfa
AF:
0.153
Hom.:
961
Bravo
AF:
0.133
Asia WGS
AF:
0.0880
AC:
306
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
May 05, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.55
CADD
Benign
6.7
DANN
Benign
0.83

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.10
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11554710; hg19: chr7-5347914; COSMIC: COSV51873396; COSMIC: COSV51873396; API